Having blood in urine that is not visible to the naked eye could be caused by various factors other than a urinary infection. Diseases such as cystitis or nephritis, certain medications, or structural issues in certain pathways can all lead to this symptom. It is important to determine where the bleeding is coming from (kidney, bladder, urethra, or ureters) in order to identify the underlying cause. Your doctor will need to conduct several tests to pinpoint the source of the issue.